Nav: Home

Digital microbes for munching yourself healthy

November 29, 2016

Hundreds of different bacterial species live in the human gut, helping us to digest our food. The metabolic processes of these bacteria are not only tremendously important to our health -- they are also tremendously complex. A research team at the Luxembourg Centre for Systems Biomedicine (LCSB) of the University of Luxembourg has taken an important step in modelling the complexity of the human gut's bacterial communities -- the microbiome -- on the computer. The researchers gathered all known data on the metabolism of 773 bacterial strains -- more than ever before. Working from this data, they developed a computer model for each bacterial strain. This collection, known as AGORA, can now be used on the computer to simulate metabolic processes taking place in the microbes and to investigate how they affect the metabolism of other microbes and that of the human host. The LCSB team publishes its results in the scientific journal Nature Biotechnology (DOI: 10.1038/nbt.3703). The collection of predictive metabolic models is available to researchers via http://vmh.life.

The bacterial species living in the human gut not only help us to digest our food, but also produce valuable vitamins for us and even affect the way we metabolise drugs. The metabolic processes of these bacteria are crucial to our health, and are highly complex: The bacteria are in constant contact with our gut cells, and the different organisms continually influence one another. Thus, they play as important a role in our health as they do in numerous diseases. Despite many advances in science, our knowledge of these microbes is still limited. To improve our understanding and to aid novel discoveries, the research team led by LCSB scientist Prof. Dr. Ines Thiele, head of the "Molecular Systems Physiology" group, has now created the most comprehensive collection of computational models for 773 different gut microbes, capturing their individual metabolisms, called AGORA. "AGORA is based on a new concept for the comparative reconstruction of bacterial metabolic models," says Ines Thiele: "It allows the analysis of a much greater number of bacterial strains than was ever possible before. With AGORA, and by including other datasets, we can systematically study the metabolic interactions within the gut microbiome and how these interactions are influenced by external factors, including the diet and host metabolism."

The first author of the study, Stefania Magnusdottir, is currently doing her PhD degree in Ines Thiele's group at the LCSB: "The basis for our paper was a thorough investigation of the literature on microbial metabolism," she explains. "We gathered known experimental and genomic data on the metabolism of 773 bacterial strains to refine and validate the computational models. Based on this, we characterised each microbe's metabolism and found that both their metabolic capabilities and our diet play important roles in how the microbes interact with each other. We can generate personalised microbiome models by integrating these computational models with metagenomic data, which can be obtained by sequencing the microbes present in stool samples of healthy and sick individuals."

"With our models, we can search, in a targeted manner, for metabolic pathways that are fundamentally important to the microbiome in the gut, and we can work out what could trigger diseases when these metabolic processes go wrong," says co-author Dr. Ronan Fleming, who leads the Systems Biochemistry group at the LCSB: "The AGORA models will now allow us to study the impact of host-microbiome interactions in specific diseases or to use them in the emerging field of personalised medicine."

Using AGORA to study the gut microbiome will involve close collaboration with researchers who are investigating the gut microbiome in the laboratory, including Prof. Dr Paul Wilmes, head of the LCSB Eco-Systems Biology group. His group has developed methods for studying gut bacteria under real-life conditions. "AGORA directs us to targeted bacterial metabolic processes to perform focused experiments, allowing precise and comprehensive modelling of processes within the gut microbes," Paul Wilmes asserts.

For Ines Thiele, the high degree of precision is not an end in itself: "We want to understand how the microbes modulate human metabolism when we modify our diet. This may give us clues as to how we may prevent, or even treat, diseases, for example by identifying dietary supplements that could modify the interactions within a diseased gut microbiome to imitate the metabolic functions of a healthy one."
-end-
The AGORA project has received support from the Luxembourg National Research Fund's (FNR) ATTRACT, CORE, Proof-of-Concept and AFR funding programmes as well as from the Advanced Computing program of the US Department of Energy, Offices of Advanced Scientific Computing Research and the Biological and Environmental Research.

University of Luxembourg

Related Metabolism Articles:

redHUMAN: Deciphering links between genes and metabolism
Scientists at EPFL have developed a new method that simplifies the processing of genetic-metabolic data by picking up changes in metabolism, a hallmark of numerous diseases like cancer and Alzheimer's.
Lipid metabolism controls brain development
A lipid metabolism enzyme controls brain stem cell activity and lifelong brain development.
Inhibition of sphingolipid metabolism and neurodegenerative diseases
Disrupting the production of a class of lipids known as sphingolipids in neurons improved symptoms of neurodegeneration and increased survival in a mouse model.
Viruses don't have a metabolism; but some have the building blocks for one
'Giant viruses' are many times larger than typical viruses and have more complex genomes.
New metabolism discovered in bacteria
Microbiologists at Goethe University Frankfurt have discovered how the bacterium Acetobacterium woodii uses hydrogen in a kind of cycle to conserve energy.
Protein controls fat metabolism
A protein in the cell envelope influences the rate of fatty acid uptake in cells.
A new model of metabolism draws from thermodynamics and 'omics'
Scientists at EPFL have developed an algorithm that can model biochemical reactions from metabolism down to RNA synthesis with unprecedented accuracy.
A new way to control microbial metabolism
To help optimize microbes' ability to produce useful compounds but also maintain their own growth, MIT chemical engineers have devised a way to induce bacteria to switch between different metabolic pathways at different times.
Parasite manipulates algal metabolism for its own benefit
Researchers from the Max Planck Institute for Chemical Ecology and the universities of Jena and Frankfurt show that a pathogenic fungus alters the metabolism of its host unicellular algae, for its own purposes: the small bioactive substances that are formed in the process benefit the fungi's own propagation while preventing the algae from proliferating.
Lack of sleep affects fat metabolism
A restricted-sleep schedule built to resemble an American work week made study participants feel less full after a fatty meal and altered their lipid metabolism.
More Metabolism News and Metabolism Current Events

Trending Science News

Current Coronavirus (COVID-19) News

Top Science Podcasts

We have hand picked the top science podcasts of 2020.
Now Playing: TED Radio Hour

Listen Again: Meditations on Loneliness
Original broadcast date: April 24, 2020. We're a social species now living in isolation. But loneliness was a problem well before this era of social distancing. This hour, TED speakers explore how we can live and make peace with loneliness. Guests on the show include author and illustrator Jonny Sun, psychologist Susan Pinker, architect Grace Kim, and writer Suleika Jaouad.
Now Playing: Science for the People

#565 The Great Wide Indoors
We're all spending a bit more time indoors this summer than we probably figured. But did you ever stop to think about why the places we live and work as designed the way they are? And how they could be designed better? We're talking with Emily Anthes about her new book "The Great Indoors: The Surprising Science of how Buildings Shape our Behavior, Health and Happiness".
Now Playing: Radiolab

The Third. A TED Talk.
Jad gives a TED talk about his life as a journalist and how Radiolab has evolved over the years. Here's how TED described it:How do you end a story? Host of Radiolab Jad Abumrad tells how his search for an answer led him home to the mountains of Tennessee, where he met an unexpected teacher: Dolly Parton.Jad Nicholas Abumrad is a Lebanese-American radio host, composer and producer. He is the founder of the syndicated public radio program Radiolab, which is broadcast on over 600 radio stations nationwide and is downloaded more than 120 million times a year as a podcast. He also created More Perfect, a podcast that tells the stories behind the Supreme Court's most famous decisions. And most recently, Dolly Parton's America, a nine-episode podcast exploring the life and times of the iconic country music star. Abumrad has received three Peabody Awards and was named a MacArthur Fellow in 2011.